 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 24, 2018 |
| Title |
A distal enhancer maintaining Hoxa1 expression orchestrates retinoic acid-induced early ESCs differentiation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Retinoic acid (RA) induces rapid differentiation of ESCs, partly by activating expression of the transcription factor Hoxa1, which regulates downstream target genes that promote ESCs differentiation. However, mechanisms of RA-induced Hoxa1 expression and ESCs early differentiation remain largely unknown. Here, we identify a distal enhancer interacting with the Hoxa1 locus through a long-range chromatin loop. Enhancer deletion significantly inhibited expression of RA-induced Hoxa1 and endoderm master control genes such as Gata4 and Gata6. Transcriptome analysis revealed that RA-induced early ESCs differentiation was blocked in Hoxa1 enhancer knockout cells, suggesting a requirement for the enhancer. Restoration of Hoxa1 expression partly rescued expression levels of ~40% of genes whose expression changed following enhancer deletion, and ~18% of promoters of those rescued genes were directly bound by Hoxa1. Our data show that a distal enhancer maintains Hoxa1 expression through long-range chromatin loop and that Hoxa1 directly regulates downstream target gene expression and then orchestrates RA-induced early differentiation of ESCs.
|
| |
|
| Overall design |
Deep sequencing of three different state cell lines gene expression and interaction of hoxa1 with the genome.
|
| |
|
| Contributor(s) |
Su G, Guo D, Lu W |
| Citation(s) |
31147716, 33581110 |
| BioProject |
PRJNA510884 |
| |
| Submission date |
Dec 23, 2018 |
| Last update date |
Mar 23, 2021 |
| Contact name |
Dianhao Guo |
| Organization name |
Nankai University
|
| Street address |
94 Weijin Road
|
| City |
Tianjin |
| ZIP/Postal code |
300071 |
| Country |
China |
| |
|
| Platforms (2) |
|
| Samples (9)
|
| GSM3528717 |
RNA-Seq of Mus musculus: EN-KO rep2 |
| GSM3528718 |
RNA-Seq of Mus musculus: EN-KO+Hoxa1 rep1 |
| GSM3528719 |
RNA-Seq of Mus musculus: EN-KO+Hoxa1 rep2 |
| GSM3528720 |
Capture-C of Hoxa1 in Mus musculus: WT rep1 |
| GSM3528721 |
Capture-C of Hoxa1 in Mus musculus: WT rep2 |
| GSM3528722 |
Capture-C of Hoxa1 in Mus musculus: WT rep3 |
|
| Relations |
| SRA |
SRP174196 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE124306_E14_RA-ed_hoxa1_capture-c_combined_interaction.wig.gz |
4.2 Mb |
(ftp)(http) |
WIG |
| GSE124306_E14_RA-induced_hoxa1_enhancer_capture-c_combined_interaction.wig.gz |
4.4 Mb |
(ftp)(http) |
WIG |
| GSE124306_E14_RNA_seq_htseq_gene_count_matrix.txt.gz |
391.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...